Waiting
by shipperscifi
Summary: When Sheppard steps through a shuddering 'Gate, ducking enemy fire, and into the tenuous grip of a flickering wormhole, he emerges on Atlantis, but not the one he left behind. He finds someone he thought lost, but unless Time itself is reordered, he'll lose them again... (Edited from my account on another site and uploaded here. Enjoy!)
1. Chapter 1

This is a story some may recognise from CD. I'm uploading it here and editing it as I go.

* * *

 ** _When a power surge hits the Stargate, his team makes it back to Atlantis, but the wormhole disengages and the traveller is lost..._**

* * *

Shots rang out, the muted shriek of energy weapons hurtling through the air and thudding into the undergrowth, sending up sprays of damaged leaves and dirt. Sheppard's team had definitely picked the wrong planet this time. Add to that two additions until Leonard's team was back up and running and this was a hell of a time for unknown natives to get irritable.

 _'C'mon, McKay!'_ Sheppard bent mid-stride, grabbing Rodney by the scruff of his jacket and pulling him up as the scientist scrambled to his feet. Behind them more shots embedded into the dirt at their heels and he picked up the pace, aware of McKay cradling his right arm, sweating with both the effort of running and the pain jarring the break.

Ahead of them, Ronan ran with Harrison and Cartwright. Teyla was back on Atlantis, a series of Athosian ceremonies taking her time away and with the extra bodies, it hadn't mattered. Now though, he wished he had an extra gun on their side. About four hundred yards away lay the Stargate, empty and silent. Waiting.

Cartwright reached it first, slinging her weapon and trusting her team-mates to cover her back whilst she punched symbols. The wormhole established with a watery rush and she straightened, tapping in the code that would drop the shield and allow them back into the safety of Atlantis.

The counter-signal bounced back and Cartwright waved her team-mates forward, running to the 'Gate to crouch in the shadows beside it. Taking aim at the shadowy figures behind McKay and Sheppard, she started firing in short staccato bursts. She could barely see the enemy, but she didn't have to, she just had to lay down covering fire for her team-mates.

Sheppard was limping, badly enough that Smith could only imagine he'd taken a round. McKay was stumbling and briefly she wondered if she should head back to help, he looked like he might go down any second but the Colonel's voice was already reaching her ears over the sound of fire, ordering his team through the 'Gate.

He was always the last through, a lesson hard-learned, or so Cartwright, new to the Expedition, had heard. He never left a team-mate behind, that was his mantra. But the the disgruntled rumour mill whispered that he'd abandoned the previous Expedition's leader to the Replicators, leaving her in their torturous hands and escaping with his own skin intact.

But from what Cartwright had seen, Sheppard lived by that personal code, and she couldn't reconcile the idea that he had left someone behind to save himself. Dr Weir had become something of a legend to the ears of the new recruits. She had watched over Atlantis for ten thousand years, or at least, her alternate reality self had done. She had saved the entire Expedition from drowning when the shields failed. She had handed herself over to the Asurans so her team could escape with a ZPM and save Atlantis, lost in the space with no power and no hope.

People still talked about her, in one way of another. It wasn't all positive, but most of it was and Cartwright wasn't inclined to like the sources that spoke ill words in the first place, let alone believe their extensive complaints. Sheppard was the source of most of their ire, but she found that hard to believe too, especially in light of a recent incident offworld. It happened almost in passing, but she remembered it clearly.

T _hey were sitting round a campfire near some ruins, babysitting an archaeology team and McKay had been talking about Daniel Jackson, lamenting that the civilian scientist of the infamous SG1 hadn't been there to examine the ruins. The conversation had moved on to old friends, and gone round the fire, drawing stories from all quarters until it had come back to Rodney and he had spoken of a woman, one who had sacrificed much to save her people. A person of intellect, wisdom and unwavering courage. The kind of thing that made up legends it seemed until Teyla had interrupted him._

 _'You are mistaken Rodney. It was Pierson, not Elizabeth who suggested that course of action.'_

 _'C'mon Teyla, she's gone now, the least we can do is make her a legend. She damn near was one too.'_

 _'Still, it is not proper to lie, even of the dead.'_

 _'Yeah, but-'_

 _It was then Sheppard spoke up, he hadn't said a word the whole way through Rodney's little story, his mouth set, his eyes trained on the flames. Cartwright was watching him when he spoke, and she saw the flicker of anguish that momentarily touched his features before he shoved it aside and replaced it with a carefully neutral expression though his words were grim._

 _'Teyla's right, Rodney, Lis'beth wouldn't have wanted to be known as anything other than she was. Let it go.'_

 _'But-'_

 _'Drop it,' Sheppard had told him, without glancing his way. Teyla had reached over, laying a hand on Rodney's arm and he had subsided with an unusually grave look. Teyla and Ronan had exchanged a glance, something unspoken passing between them._

One thing was for sure, the memory of Weir's death, though it was almost two years ago, was still a touchy subject for Sheppard and obviously offlimits outside the team. It made her wonder what had _really_ happened that day.

Harrison was backing up, laying down cover fire as Ronan ran back and grabbed McKay from Sheppard, leaving him to carry his own weight instead of two on his wounded leg. He glanced back once but Sheppard waved him on. _'Go, go!'_ he shouted above the sound of fire and tearing undergrowth.

Ronan jerked his chin curtly at Cartwright and Harrison, ordering them through the 'Gate. He and McKay were barely twenty feet away, the Colonel lagging behind, turning to aim staccato bursts of fire at their pursuers. Another shot hit the 'Gate and Ronan fixed her with a brief glare. The scientist was cradling one arm, his weapon slung. The angle was bad, a break for sure and she briefly wondered how he'd kept going. Ronan didn't watch to see she obeyed orders, he let go of McKay and turned, firing on the enemies, releasing her and Harrison from guard duty.

Backing up, not letting up on the rate of fire until the last second, Cartwright backed across the threshold, right after Harrison and McKay. The ride was rough, and she felt like throwing up as she fell back onto the smooth cold floor of Atlantis' Gateroom, gasping a breath into burning lungs. Behind her medics were already swarming but McKay refused to leave until the last two stepped through. Ronan came first, the jerky ride through the wormhole leaving him swaying slightly, but he kept moving backwards, waiting for the Colonel to follow.

The event horizon flickered, almost as if the 'Gate were losing power. Sparks flew and electricity arced, wrapping itself around the 'Gate.

' _Back!_ Everyone get back!' It was McKay, but they were already retreating, drawing back instinctively. The 'Gate itself shuddered, shaking the floor and the walls around them. Cartwright tried to stagger to her feet, feeling her arm caught in an iron grip as Ronan backed up, dragging her with him.

The wormhole stuttered, a steady whine filled the room and, for a moment, everyone in the vicinity held their collective breaths.

And then the system blew. With a series of muffled explosions the event horizon disappeared and the wormhole collapsed. No other traveller crossed the threshold, and in the horrified silence that followed, a single thought ran through the minds of all those gathered nearby.

Sheppard was gone.


	2. Chapter 2

Shockingly short chapter, I'm afraid.

* * *

 ** _A familiar voice broke through the pain, and he grabbed it like a lifeline, all the while his mind screaming that it was impossible..._**

* * *

They were firing again, running footsteps coming closer and he could hear their voices now. The event horizon shimmered, ripples spreading outwards as Cartwright disappeared after McKay and Harrison, her anxious expression disappearing behind the illusion of water.

A moment later Ronan, with Sheppard himself only a few feet away, stepped through, his eye never leaving the enemy, his weapon never silent. The Colonel turned, firing a random spray, the pain in his hip almost unbearable. He was staggering now, almost unable to keep on his feet.

Another shot was loosed and something slammed into him from behind. All the air was driven out of his lungs and they burned, trying to draw oxygen in and failing. His brain was slow, refusing to catch up with his body and Sheppard staggered another step, night closing in fast. It took another heartbeat to realise it was his mind, not the sky, casting shadows and a bolt of fear shot through him, flooding his system with adrenaline and propelling him into the fluctuating event horizon.

An energy bolt hit the 'Gate, overloading its capacitors and charging the system with more power than it was prepared to handle. Like water it ran into every available outlet, blowing power conduits on both ends and throwing the wormhole off-course. It drew more power from the star it interesected, expending the energy by pushing the limits of its capabilities.

Inside the wormhole, Sheppard was tossed as if he rode a stormy ocean. When his form coalesced and he emerged, he was thrown out like a ragdoll onto the cold, hard floor of Atlantis' Gateroom. By sheer chance, the iris shield had been blown by the amount of power that poured into the 'Gate system and he made it, whole but not undamaged, a prone figure at the foot of the steps to the control room.

Everyone nearby froze. They had evacuated the Gateroom when the unexpected connection had made the wormhole unstable, blowing power conduits and showering the soldiers below with sparks. A host of weapons remained pointed at the 'Gate but not a single shot was fired. Despite the rapid exit of their visitor, there wasn't a person present who didn't recognise him, despite the unfamiliar uniform.

A medical team was called and Atlantis' leader ran down the steps, crouching by the prone form. Loren called out his objections, but she ignored them, telling him to call the Colonel. She touched his shoulder, calling his name. 'John, _John?_ '

He skirted the edge of unconsciousness for a moment. Every muscle felt as it were on fire, but he was breathing again, regardless of the pain and he considered that a bonus. He felt the darkness closing in around him and fought it. A voice pierced the fog, a metaphorical bullet to the brain. It hurt worse than his injuries to hear it, and he wondered if he were delusional. Somewhere, the logical centre of his brain screamed that this was impossible.

He didn't care. He clung to the words, the touch of a hand on his shoulder, straining to listen, using her voice to pull himself back to the world. But then others arrived, a cacophony of words, hands lifting and the pain rose in a wave, breaking over him. Another voice broke in, even more familiar than hers.

 _'Lis'beth, what the hell-?'_

 _'I don't know-'_

 _'Get back, you have no idea-'_

 _'He's hurt, John.'_

 _'It could still be-.'_

 _'No,'_ an unknown voice cut in, _'the scan is clear.'_

Her voice again, _'keep us informed.'_

The darkness took him this time, tossing him into a world confusion and dreams until something cold pressed against his neck and the sedative flooded his system, driving away all thoughts.


	3. Chapter 3

_'What I said- you gotta stop doing that.'_

 _'I'm not-'_

 _'Yes, you are,' he interrupted, 'you do it everyday.'_

* * *

'Where the _hell_ did he come from? I don't remember getting shot up like that, and did you see that _uniform_? Must be, what, least four years old, although it doesn't look right. There's something wrong here-!' Sheppard's words spilled unchecked.

He paced around the briefing room like it was a cage, black hair wild from fingers constantly running through it. He wasn't normally this unsettled, but seeing yourself thrown through the Stargate, unconscious and injured, wasn't a normal occurrence, not even for the 'Gate travellers. And Elizabeth, true to form, had rushed to the injured's side, skipping protocols. Sometimes, he thought she took compassion too far. But then she would, wouldn't she? It reminded her she was still human.

Hell, she was more human than he was even when she was a Replicator.

'I don't know, John, but you're not helping, please sit down.' Elizabeth's calm voice cut across his words, It was normally McKay that went off like this, but this was John, and her tone belied her emotions; the sight was unsettling.

He almost refused, but caught her eye and changed his mind, sinking into a chair across the room from her, exchanging a look that offered a silent apology. This wasn't an easy situation for any of them and the cause of it was lying in an infirmary bed, hovering somewhere between life and death; closer to the former if the optimistic doctor's words were to be believed.

'Rodney, have you found anything?' Elizabeth turned her attention to the physicist who had said nothing, waiting for Sheppard to come down before he opened his mouth. The years had given him a gravity and patience no one would have thought possible when he first joined the Stargate program.

'Well, it's kind of hard to say. We've run a 'Gate diagnostic, and we're underway with a local system check, in our vicinity as well as the area around Elaras, where the traveller came from. We haven't turned up anything much as of yet except evidence of a large power surge at the time of the wormhole that brought Shep-, that is, the _other_ , Colonel Sheppard to our door. We won't know anything more for at least eight hours, if the, er, _other guy_ , doesn't wake up before then.'

'Archer?'

The tall dark-haired doctor was standing quietly behind his place at the conference table. He rarely sat down, except in the mess hall, if he was seen there at all. Archer, known by his last name so well that his first was almost forgotten, took his meals on the go. He worked or trained or taught himself something new almost every hour he was awake. Despite that, he was never stressed and never hurried. If there was an emergency, he ran, at all other times, he strolled.

'Jonathan Sheppard,' he began, cutting out all variables of _the other guy_ in one breath, 'is making a slow recovery, unsurprising considering the extent of his injury. The surgery was successful and my main concern at this stage is infection, assuming we can avoid that instance, he should be awake sometime tomorrow.'

'Good. Will he be fit enough to answer some questions?'

Archer nodded, 'but I want to keep the interview time short, I suggest you consider what to ask him beforehand, he'll most likely tire quickly.'

'And he is... Who we _think_ he is? It's confirmed?'

Another nod, 'so far, although the genetic analysis won't be complete until tomorrow. However, other factors such as fingerprints, blood type, morphology, internal scans, all track, but only up until about six years ago. However, that does not pinpoint his origin, merely limits the time from which he could have come.'

Elizabeth nodded, tapping her pen on the pad in front of her. Despite the high level of technology at their disposal in Atlantis, there was a new-found tactile comfort for her in old-fashioned paper and ink. From across the room Sheppard watched her, wondering if she would ever believe she was human again.

For a woman who could sink herself into the mind of a computer, or connect with technology at will, it made a kind of sense to use her tactile sense more. It had taken a year of fighting to keep her on Atlantis without challenge, Stargate Command and the IOA nearly two years to trust her, three to place her in a position of importance on Atlantis and she had only been back in official command for six months.

It was a trial period that this incident may blow out of the water if she continued to second-guess her decisions on it. He made up his mind then and there to back her on this one because, despite the demeanour she presented to the outside world, there were times she doubted herself to the point of considering resigning.

It was a disturbing side-effect of her time amongst the Asurans and her dual existence with the nanites that swarmed in her bloodstream. With the presence of his own doppelganger, not an imitation but the real thing, as far as they could tell, he understood her fear a little more now, the fear that one of her own duplicates would show up, corrupted by their connection with fractured factions of the Replicators. They had downloaded her mind before, an incomplete and corrupted version- she had seen to that- but nontheless, he knew it worried her.

She wasn't the only one with that concern; and she had only _heard_ the stories of her duplicates presence on Atlantis. The rest of them had actually _been_ there, and then, when they'd finally rescued her, almost by accident and years after they thought her gone... His face darkened along with his thoughts and McKay happened to glance in his direction.

He could guess the tone of Sheppard's musings, and turned away, leaving him alone with them. Archer and Weir were still talking and their conversation ended with the meeting. McKay took up the slack then, leading both Archer and his assistant, Gardner, away from the briefing room on a flood of chatter, tactfully leaving Sheppard and Weir alone.

John hadn't moved and Elizabeth leaned back in her chair, regarding him with narrowed eyes. 'Is this another I-blame-myself moment?'

He looked up, arms still crossed over his chest but didn't move.

'Because if it is, your timing couldn't be worse,' she added. 'I need your help on this, John.'

'Yeah,' he drawled , leaning forward slowly to lean on the desk. 'I think it still holds.'

'What?' she asked, confused.

'What I said- _you gotta stop doing that.'_

'I'm not-'

'Yes, you are,' he interrupted, 'you do it everyday.'

She closed her mouth, not bothering to deny his statement, there was no point, he knew her too well.


	4. Chapter 4

_Sheppard opened his eyes, finding a face to match the voice. She was sitting in the chair next to the bed, watching him. For a moment, he couldn't breathe. She wasn't the first dead face he'd seen, but did it have to be_ her _?_

* * *

Sheppard awoke to the familiar sight of the infirmary ceiling. Memories flickered- Elaras, the natives, their energy weapons, the guttering wormhole and the blinding flash as he was propelled across the galaxy and into the blinding pain of being thrown, already injured, across the floor of the Gateroom. Something else flickered around the edges of his memory too... An hallucination, he figured, a memory dredged up from somewhere. He pushed aside the thought, _wishful thinking._ He was surprised, a little, to realise he remembered her voice.

He sighed, shifting uncomfortably. Every muscle ached, and somewhere, lurking around the edges, he could feel the barest hint of pain. Whatever they'd given him would be wearing off soon, and he wasn't looking forward to it.

'Doc?' he croaked, his throat dry. He tried to swallow and speak again but it was no good. He closed his eyes for a moment, waiting for Keller to appear. A gentle hand landed on his shoulder and a voice spoke quietly.

'Here.' A straw touched parched lips and he drank, easing the burn in his throat. He coughed, tried to sit up and the same hands helped him. He gritted his teeth against a sudden surge of pain and fell back against the pillows. He wasn't sure he should open his eyes.

'Better?'

It was impossible, but he couldn't shut her out forever.

Sheppard opened his eyes, finding a face to match the voice. She was sitting in the chair next to the bed, watching him. For a moment, he couldn't breathe. She wasn't the first dead face he'd seen, but did it have to be _her?_

Guilt washed over him in a wave.

'E-Elizabeth?'

A smile and she nodded. She wore a red t-shirt, like always, but her hair was longer than he remembered, caught back at the nape of her neck, dark curls cascaded over one shoulder. She looked tired but the smile was the same, humour lurking forever in her green eyes.

'You're dead,' he said flatly.

 _And this is a trick. It has to be,_ he thought to himself.

She looked confused for a moment, then shook her head. 'No, John, I'm alive. I think Archer might have a problem with me walking around his infirmary if I weren't,' she added with another smile.

'Archer?'

'Atlantis' chief medical officer. John, I realise this isn't going to be easy, but... This isn't your Atlantis, at least, we don't _think_ it is. And, if you're up to a few questions, we'd like to find out how you got here and where exactly you're from.'

It was his turn for confusion. Pushing himself further up in the bed, he winced and looked around. Medical personnel wandered to and fro, most of the beds were empty and at the foot of his stood two men, one he didn't recognise but the other he knew well. Rodney McKay.

'McKay?' he questioned, warily.

'Hey there,' Rodney lifted a hand, obviously ill-at-ease and Sheppard threw him a narrow look, wondering what was going on.

'I don't buy it,' he replied, looking from one face to another. 'we dialled Atlantis from a normal 'Gate, no weird tech, nothing. Why would I be somewhere other than _my_ Atlantis?'

Elizabeth shrugged, 'there's a number of potential reasons, Rodney can tell you more than I, but we won't know for sure, or how to send you back unless you give us a little information.'

Sheppard nodded, looking unsettled and shifted in the bed. 'Yeah, well, you'll have to forgive me, but I've done this one before, and it's not that I don't believe you-' he paused, caught by an outright lie, 'okay, so I don't believe you, but you gotta understand-'

'I do,' Elizabeth cut him off with a wave of her hand. 'And I would love to take the time to convince you, but you need to understand that we're working under a time limit here. I've grounded all crews and offworld teams have been ordered to stay put so we can extract information from the 'Gate system.' She leaned forward, her face earnest. 'But I can't just leave my people out there, John. I'm not asking you to compromise security, but I do need you to tell Rodney everything you possibly can. We can't work this out without your co-operation.'

Slowly, Sheppard nodded, running through the information in his head. He could see nothing that would breach security in his story, and if she was telling the truth there were people stranded offworld because of him... As long as he stayed aware of the fact that they could be lying and watched what he said, watched _them_ for lies or discrepancies, maybe he could find out what was _really_ going on.

He found himself staring at her, and looked away, unable to juggle his thoughts to place her back in Atlantis. The only time he'd seen her here after he'd left her in the hands of the Asurans, was as a Replicator, and it was more than possible that he faced the same situation now. Still, when he replied, his eyes sought her face again.

'Okay,' he finally capitulated, 'although I don't actually remember arriving here. Just... flashes.'

 _Of your voice,_ but he didn't say it out loud.

'That is unsurprising,' it was the stranger, his dark voice reminding Sheppard strongly of Ronan. 'You were thrown through the event horizon with enough force to shatter bone. You are lucky to be alive Colonel Sheppard. As it was, the worst injury you sustained is synonymous with the discharge from an energy weapon.'

John nodded, 'we were taking heavy fire. Never got to meet the natives, they seemed to take offence that we even set foot on their planet. They attacked, we ran. I was the last through the wormhole,' a sudden thought hit him, 'my team? Did any of them-?'

'No one else came through, Colonel. Only you.'

John nodded slowly, wondering if they'd made it back safely to Atlantis. The right one- assuming this incarnation of Weir wasn't lying. _Elizabeth Weir_. If this were another Replicator trick, as unlikely as that seemed, he'd spend the rest of his life chasing down and eradicating every damn faction. He'd wipe out any information they had on her, every trace of her thoughts or mind or personality from their systems. And then he'd go find and destroy the replicated version of her, frozen outside a spaced 'Gate somewhere in the Pegasus Galaxy.

'Sheppard,' it was Rodney, curt as always, 'I need you to tell me everything you can about their energy weapons.'

'Their _weapons,_ McKay? We were running for our lives, I didn't stop and ask them for blueprints.'

'Ha ha, you're as funny as our own dear Colonel Sheppard.'

' _Rodney!_ ' It was Elizabeth, her voice carrying a warning tone.

' _Your_ Sheppard? So what is this, an alternate reality?'

'It's a possibility,' she sighed, drawing his attention back to her. 'One of several, and we're still working on how this happened. Which is why we need any information you can give us.'

John nodded, 'so where am... _I_? Offworld?'

She shook her head, 'no, he's here on Atlantis, but we thought it best you woke up to familiar faces _other_ than his.'

'Familiar dead faces,' he replied somberly. His eyes were on her again, and Elizabeth wondered what the hell had happened to her in _his_ world that he would carry such a burden of guilt. His face was transparent, and he almost acted as if he shouldn't meet her gaze, even though he couldn't take his eyes off her.

'So I gathered. Rodney wants to ask you a few things now, but I'll come by later, see how you're doing?'

'Sure,' he watched her stand and walk away, the stranger turning on his heel to follow her. They headed for the door, talking quietly whilst Rodney lifted a tablet onto one arm, his expression enquiring. But he didn't receive an ounce of Sheppard's attention, not until she left the room.


	5. Chapter 5

_If two Sheppards confuses you- in the narration Sheppard is the future one, John is the past one. Sometimes, in the speech bubbles, the speaker mixes that up. In the narration it will remain the same._

* * *

 ** _Elizabeth Weir, the future Elizabeth, was living a dual existence, proving her loyalty, even her humanity, to herself and those around her every day; and it was killing_ his _future self._**

* * *

McKay had long gone and Sheppard found his way back into sleep, still sitting up against the pillows and riding a tide of painkillers. His dreams were fractured and unreal, reliving the events around Elizabeth and her loss. Liam, his hands round her throat... Oberon, his hand in her head... Asurans surrounding her... Carter apologising for declaring her KIA... her mother's tears when he came back to Earth and told her... Carson's funeral, only it wasn't Carson, it was Elizabeth and he watched her body dissolve into nanites... they swarmed over Atlantis and he could hear her crying as they destroyed everything she died to protect...

He awoke with a start, stifling her name on his lips. He had hated the nightmares, they had slowly slipped away and he hoped backtracking into them was only temporary. He glanced around, shifting into a more comfortable position and finding a mirror sitting beside his bed. It was the same tousled hair, dark eyes and almost insolent expression he saw every morning he shaved. There were differences too, including new scars, but no mistaking Colonel John Sheppard in an updated, he assumed, uniform. His doppleganger sat with legs outstretched, ankles and arms both crossed, watching him indolently.

'Last time I met myself it didn't go too well,' Sheppard spoke first 'So how're we gonna to do this?'

'You're John, I'm Sheppard. McKay's idea, and it seems to have stuck. I can't say I appreciate it from some quarters,' he added, thinking of one particular person who had taken calling him _Sheppard_ again. 'So,' he drawled, 'what's your story?'

'I already spoke with McKay-'

'More general. Give me a context, a quick run down of the Atlantis you live on,' he saw the hesitancy in his double's face and carried on with a slightly sarcastic note, 'you don't need to breach security, and we're _not_ Replicators.'

'I never said you were!' John protested his innocence.

'You were thinking it though,' came the reply, delivered with a careless conviction.

John considered, then nodded, he was right after all. 'Okay, let's see. I'm a Colonel, the IOA's still a pain in the ass, the Wraith are still bouncing around the galaxy, the Asurans are scattered and the Athosians have a nice little homeworld now we've managed to get a number of them back. On Atlantis, Keller's in charge of the infirmary, McKay's still in charge of research, Carson's dead, Heightmeyer too, Woolsey's running things, and we... lost Elizabeth to the Asurans a couple of years ago.'

Sheppard's eyes narrowed, as if he were thinking something over. 'Teyla's had her baby? A boy, second name John, first name Torren? '

'Yeah,' came the wary reply, he had deliberately left Teyla and her kid out of the conversation, not wanting to put them at risk, but his copy obviously knew them.

Sheppard nodded, 'Carter ran Atlantis for about a year, she was recalled. How recently?'

'Nearly a year ago, why?'

'Because I think I'm beginning to get an idea of where you're from and I can't say I like it,' he lifted a hand and touched the communicator at his ear. 'McKay? I need you in the infirmary,' he paused, ' _now_ , McKay. Yes, I know, but I think I may know what you're looking for.'

Irritatingly, John found himself left out of the loop, Sheppard standing there silently without a word until he could hear footsteps outside the infirmary. McKay stepped through, followed by another unfamiliar face and tailed by Elizabeth. She hung back at the foot of the bed as McKay joined them.

'What is it that couldn't wait?' he asked impatiently.

'I think our visitor here isn't from another reality, in fact, I think he's from this one, six years from our own past.'

'C'mon! You think I haven't thought of _that_? But the events don't match up! You've never been to Elaras, and you've never mentioned being thrown through time, other that that incident with the forty thousand yea-'

'I remember that,' John interrupted from the bed, 'are you telling me I've landed myself in the future again?'

'Possibly, but our Sheppard's timeline doesn't match yours, which indicates alternative reality- Unless it's an alternative _timeline_ that we're in. Your going to Elaras could have changed our whole past, but how would that event have started-?' McKay punched his tablet, frowning as he read a paragraph of Ancient text on the Stargate system and it's anomalies.

'Elizabeth, didn't you something about a ripple effect-?' Sheppard asked, but McKay cut him off.

'If- Oh yes! _Yes_! If the surge affected the 'Gates around Elaras and Atlantis, the bubble would expand- I gotta- Scuse me-' and he turned, heading for the door, head bent over the tablet across his arm, muttering to himself. The stranger followed, leaving John alone with Sheppard and Weir.

'So, we're what? One _potential_ future?' Sheppard demanded and Weir looked up from the end of the bed, her face pale, shadows darkening her eyes. Sheppard looked her over, concern lacing his features.

'Sit down 'Lis'beth, before you fall.'

'I'm fine,' she looked him square in the eyes and let go of the bedframe, as if proving it to herself as much as to him. He shot her a sour look and indicated the chair again.

'I'll call Archer,' he threatened lightly.

Elizabeth suppressed the urge to roll her eyes and gave in, taking the proffered seat, but John noticed that the moment she sat down some of the tension in Sheppard eased. He wondered if she were over-working herself again. He remembered swinging by her office, every night he was on Atlantis, before going to bed, just to check she was getting some rest... He shook his head, this wasn't right!

'I can't be from your past,' he suddenly spoke, biting back the pain his words brought. 'Our Elizabeth is- _dead_ ,' he nearly choked on the word. Admitting it here in front of her, admitting he failed to keep her safe, made it harder to say.

'Not if I'm right,' came Sheppard's reply.

'Jo- Sheppard,' the warning tone again, and it wasn't directed at him, it was aimed at his counterpart. 'If we are only a _potential_ future, we can't risk him taking back certain information.'

'Like where you are? Where we _found_ you? If this is only a _possible_ future we're standing in, Elizabeth, we need to limit the changes that are going to be made to our reality once we send him back. If we even can!'

'That's no excuse, not until we know-'

But he cut her off. 'There's no excuse for leaving you with the damn Asurans for years either! And I'm _not_ letting it happen again.' His voice didn't rise, but the tone brooked no argument.

' _What_!' John exploded into the conversation, looking between the two of them with a sense of dismay and anger, 'are you telling me that, _in my time_ , Elizabeth is still _alive_? The Replicators lied?'

' _No!'_ Elizabeth interrupted swiftly. 'I knew the Replicators you met, John, they were honestly trying to seek Ascension, they wanted to do no harm but Oberon made _everyone_ believe I was dead. He wasn't as dismissive of Ascension as he had others believe. He was searching for a technological means, one that wouldn't involve enlightenment because Oberon only wanted one thing, to find the Ancients and make them pay for what they did to his people. To him. He was blinded by hatred.'

'So he-' The words stuck in his throat, he couldn't say them. He has _used_ her? He remembered the Replicator Weir saying something about her being the link. A machine, but with free will.

'Experimented on me,' she replied calmly, 'for quite some time. I was the way forward for the Asurans, a way to break their programming. They wanted free will, and I had it, but I could also link with the others, in many ways I was a Replicator. I still am, but more of a, a... _hybrid_.'

'You're not a hybrid, Lis'beth,' Sheppard cut in grimly. 'What did I say?'

'You do it too,' she shot back and he sighed, scrubbing one hand over his face.

'Alright,' he acquiesced. 'Just, get some rest will you?'

'You won't say anything?' she asked.

'I'll do what I have to, same as always. Same as _you_ ,' he added with a wry smile. He reached down, pulling her to her feet and John looked away, he liked his personal space but apparently his future self didn't mind Elizabeth _in_ it. They didn't do anything overt, just stood a little too close, exchanged a glance that said far too much. Then she walked away, her pace slow, heading for the door. She glanced back once, but didn't try to dissuade him again and disappeared into the corridor.

'What's wrong with her?' John asked, his voice low.

'Huh?' Sheppard broke away from his reveries, his eyes had been on the door even after she had gone. Elizabeth Weir, the future Elizabeth, was living a dual existence, proving her loyalty, even her humanity, to herself and those around her every day; and it was killing _his_ future self.

'Elizabeth. What's wrong with her?'

'Nothing. At least nothing that can be fixed. She's been helping McKay; sinking herself into the 'Gate systems, and tracking down all the information from your journey here. she wasn't joking about being a hybrid, although she's not. She's our biggest asset, although the IOA see her as our biggest threat. Even she does at times.'

'If they feel that way, I'm surprised she's back in charge.'

'It only happened six months ago. And I have veto power if I think she has been compromised at any point. The IOA are idiots and couldn't see an asset if you shoved it up-'

'I get the point. I don't need the imagery.' His double grinned at that, the first smile John had seen on his face. 'Will she be okay?' he asked.

'Yeah. Communicating with her nanites directly takes effort; and denying her sleep was one of Oberon's favourite forms of entertainment when the research stalled. When we found her, we didn't think she'd live, despite the nanites. But she's okay now, she's just been working too hard.'

'Yeah, about that. Where is she in my time? _Forget_ what she said, tell me where she is. This future might be unstable, but my present isn't, and no matter where time goes from here, I can save her. If you help me,' John said, his tone urgent. He wouldn't leave here without that information, _if_ he could leave here at all.

Sheppard watched him for several long moments, 'this information can't go any further than the two of us. If I tell you, this is _all_ I'm telling you. I don't want to affect this reality any more than I have to. If I do, there's no telling what might happen.'

'I understand.'

'No, you don't. You can't simply go home and rescue her, you have to wait for the right time, you have to leave her in Oberon's hands. Can you do that? Can you leave her there?'

He didn't want to, in fact every fibre in his body rebelled at the idea of leaving a member of his team, his _family_ , in the hands of the enemy, especially an enemy like Oberon, but he had no choice. Without Sheppard's intel, he may _never_ find her again.


	6. Chapter 6

**_When they'd brought her home, the first time she had been allowed to get out of bed, she had headed directly for the nearest window to take in the view of the city and its boundless oceans... he let himself believe that somewhere in that mess of human and replicator... Elizabeth Weir still lived._**

* * *

They talked for nearly an hour, John repeating back to Sheppard everything until he was sure his doppleganger had memorised the details. He left John sleeping once more, worn by the effort of extended conversation and went in search of Elizabeth, hoping to find her likewise. But when he entered their quarters, he found her wide awake.

'You told him.' It was a statement, not a question.

'Of course I did, what did you expect me to do?'

'Nothing else,' she was still staring out the window. In lieu of the view on the balcony outside her office, she chose the waves outside her windows. It had always been that way. When they'd brought her home, the first time she had been allowed to get out of bed, she had headed directly for the nearest window to take in the view of the city and its boundless oceans. She missed the old waves, she had told him quietly, but she was glad he had chosen this view on their new world.

And he'd let some of the tension go, let himself start to believe that somewhere inside the mess of human and replicator that they had rescued, Elizabeth Weir still lived. She'd proven it too, over and over again in the years since she had returned to them. Despite all she had done though, the IOA still didn't quite trust her.

He remembered the research lab where they had found her; all stark lines and white walls. Clean room. It had carried the odour of death, a purely psychosomatic reaction he knew, but still, he had _felt_ it. Elizabeth had been contained in a large cylinder, her life held in a kind of suspended animation. They had radioed base, secured the area and retrieved the pod.

It wasn't until much later that they realised she was actually awake in there. No cryo, no suspension of time, she was living inside the tube, thinking and feeling and watching them all. She said afterwards that Snow White in her glass coffin must have felt the same. Ripping out her pod had activated her emergency wake-up procedures and they had been lucky not to kill her when they severed her support systems.

He hadn't felt like Prince Charming, and instead of a kiss, he'd ripped her pod out of the lab and dragged it home like some trophy. She had shaken her head, told him to stop being so melodramatic, told him it wasn't his fault. His guilt irritated her at times, actively hurt her at others. There was nothing he could say to alleviate the pain on either side.

She turned then, shaking him out of his reverie and walked over, automatically slipping her arms around his waist and leaning into him with a soft sigh. It hadn't been like that at first, when she hadn't been able to trust herself around _pure humans_ , as she called anyone untouched by nanites. But she had only admitted it to him and Ronan; Ronan had scoffed outright at the claim and he had seen the surprise in her eyes. The big Satedan had leaned foward then, deliberately taken her hand in his.

 _'I came to say goodbye, after the surgery, when the doc said you'd never wake up. Thanked you for letting me stay here. That action gave me back my life. You didn't know me, had no reason to trust me but you did. I'm thankful for the chance to repay you. I trust you, Dr Weir. If you don't trust yourself, then trust_ me _.'_

He had damn near hugged the man for that, for pulling her back from the precipice. He was biased, and she knew it, but Ronan saw things clearly, he always had and she believed him when he told her he trusted her. He understood her doubts, he knew what she had gone through the first time. She was terrified of losing herself, of becoming the monster she tried to protect Atlantis from.

Later, Teyla, who became her confidant, helped guide her back along the road to find her humanity. Something she had thought lost, but something no one else ever considered had gone missing. He hadn't left her side in three years, and he wasn't going to start now.

After a moment, she stepped back.

'Were you really like that?' She had been crying, her eyes bloodshot, and she made no attempt to hide it, unashamed of her tears. But now they were dry, her voice demanding.

'Like what?'

'Like him... carrying around that-that much _guilt_. From the look on his face, John, he may as well as have killed her himself when he left her behind.'

He sighed and reached out, pulling her back against him and wrapping his arms tightly around her shoulders. 'I wouldn't go that far, but sometimes it almost felt that way. I couldn't even give you the same mercy I showed Sumner, I didn't fight harder with Carter to make you a priority sooner and then I believed your Replicator duplicate too easily...'

He buried his face in her hair. She smelt of the ocean, and the wind, clean and fresh and he breathed her in, finding his way through a story he had given her before and would again. '...And then I guess, I wanted to believe. If you were dead, Oberon couldn't hurt you anymore, and my chances of finding you, lost somewhere in the Pegasus Galaxy, were frighteningly slim. I swore I would hit that kill switch, I know I fought Rodney to activate the nanites _at all_ but I wanted you back, so badly that I didn't even trust my own judgement. And then, on the Asuran homeworld, I left you behind...'

Her arms had wrapped themselves around his waist and they tightened at the sound of his words. 'None of it was your fault. I ordered you to go.' Everything he said was true. He hadn't sworn it aloud, but he had nodded when she told him to use that switch, and it was all she had needed. When she made him leave, she knew he would do it. He'd made that promise a long time ago.

'But you were _terrified,_ I could see it. I left you like that, alone and scared and in the hands of the enemy.'

She raised her head, green eyes wide and bright and serious, when she spoke, his heart skipped a beat, knowing she wasn't lying, that would carry out her promise. She couldn't live this way, and neither could he.

'If you don't let go of the guilt, John, I'll leave. I'll have to, because we, _what we have_ can't survive either. It'll turn bitter and we'll lose each other. And I don't want that, John, I'd rather have you as friend in another _galaxy_ than a stranger here beside me.'

He nodded, turning over her words before replying, 'I'll try. I won't promise, I won't lie, but I will try, and if I fail, it won't be because I didn't give it everything. But you have to let go of your mistrust, 'Lis'beth, because this won't work only one way.'

'I trust you, John,' she looked puzzled, unable to grasp his meaning. Her distrust so deepseated, she didn't even recognise it herself.

He shook his head, his voice gentle, ' _yourself_ , Elizabeth, you don't trust yourself.'

Shocked eyes searched his face, assuring herself that he was telling the truth. She found no lies there and lowered her gaze, absorbing what he'd said.

'I'll try,' she replied, unconsciously echoing his own words. 'I promise, I'll try.'


	7. Chapter 7

_**The future they had built, finding Elizabeth and rebuilding Atlantis, was in danger, keeping their bubble of reality could fracture the universe...**_

* * *

McKay practically ran into the office beyond the control room, the tablet computer tucked under his arm and a wild look in his eyes. 'Elizabeth!' he practically shouted the name to the empty office before tearing on through to the balcony.

Outside, John and Elizabeth stood, beyond them the sun spread a cloth-of-gold over the waves. An early morning breeze had sprung up and the peace shattered as Rodney came running out of her office.

'Sheppard! Elizabeth!'

'McKay! What the-!'

Rodney drew a breath, but the wide-eyed look remained, and he appeared anything but calm, his nerves torn more raw by the data he had finally compiled only moments before than the all-nighter he had pulled on an empty stomach and caffeine.

'The timeline's going to collapse,' he babbled and took in blank faces for a second before launching into an explanation. 'The other Sheppard's time is encased in a _reality_ _bubble_ , it's resolving the changes in the timeline between his present, his past _and_ his future. That's why his uniform isn't what we remember. It's altering _his_ past as well as _ours_. The bubble hasn't reached us yet, it's still expanding through the timeline. Sheppard coming here- impossible though it sounds- actually created the alternative past where he went to Elaras. That single trip through the 'Gate send ripples through time in both directions! It _has_ changed his past, but more importantly it will change _ours_ , possibly beyond recognition.'

'So, the reality bubble has extended far enough that he visited Elaras and I didn't?' Sheppard asked incredulously.

'Yes.'

'But we won't remain unaffected?'

'No. The trouble is, the 'Gate system, having been built by the Ancients, was created to avoid anomalies of this kind, otherwise potential realities would intersect and multiply until they finally, uh, overloaded this universe, causing it to collapse in one itself,' Rodney finished.

'And that means-?'

Weir stared, the nanites inside her brain wirelessly taking the raw data McKay had downloaded into Atlantis' computers and running calculations before extrapolating the probabilities.

'Basically it means that the 'Gate's failsafe systems will kick in and either collapse the bubble or _this_ timeline before either one breaches the safety protocols,' Rodney explained.

'Okay, why hasn't it happened already? And can we stop it?'

'We can't.' It was Elizabeth, breaking her self-imposed silence. 'The lag time was put in place by the Gate builders to enable potential timelines to be resolved by their inhabitants prior to collapsing.' She turned to John, 'I found something in the 'Gate system after Sheppard's trip here, but I didn't know what it as until Rodney just told us about the reality bubble.'

'Okay. I think I'm getting this. What do you mean, a 'lag' time?'

' If the conflicting events within the bubble could be resolved by its inhabitants, there would be time to do so, if not, a collapse would be forced by the 'Gate system in order to prevent multiple realities coming into existence. It's likely we already have two co-existing timelines branching from this end of the reality bubble. Minimum. There's likely to be more, and they'll multiply.'

'Uh, yeah, exactly.' Rodney still wasn't used to the wealth of knowledge and computing power that Elizabeth had practically at her fingertips. And Sheppard being smart was something he would never get used to anyway.

'So what do we do?' John asked, looking between them.

'To stop the collapse? Nothing.' McKay replied, 'we have no way to find the conflicts let alone resolve them in time.'

'No,' Elizabeth interrupted, her words careful, 'but we _can_ stabilise this particular timeline, make it more likely that the bubble will resolve events in our favour. It's unlikely to be exactly the same, but major events should remain static.'

'How?' both of them asked at once.

'We send back Sheppard with enough information to steer events along this timeline. We don't have enough information to find and resolve the conflicts, but if we know how things should unfold, or rather if _he_ does, he can make sure they happen. For the most part, after all, the conflicts are likely to be within the confines of his personal timeline.'

'That has... a really bad chance of working. On the bright side,' Rodney added, 'if we are living in an alternative timeline, we won't notice.'

'Oh, that's just fantastic. Thanks Rodney,' Sheppard replied, sarcastically.

'He's right,' Elizabeth spoke again, 'there is no way to stabilise our present reality with any certainty. We can only hope things will turn out the same. John,' her voice turned serious, 'we should let things run their course. I know what I said, but I'm not sure we have the right to resolve this in our favour.'

'No! That's unacceptable!' he protested.

He felt a hand on his arm, and slender fingers wound tightly around his own as her other hand crept into his. 'I'm sorry, John, but I won't risk destabilising the whole of reality. We have to allow this timeline to dissolve, and we do that by sending Sheppard back, as soon as possible. His presence here is only extending the lag time.'

' _Good!_ It'll give us time to think of a plan where we don't leave you behind again!'

She didn't answer, turning to Rodney. 'Can we do it? Can we send him back?'

'Well, yeah, sure, that's the easy part. I have to make some calculations, alter a few programs in the dialling computer but it should be-'

'Good. Do it. I'll check with Archer to see if our guest is well enough to depart.'

Rodney nodded, hesitating. Elizabeth lifted an eyebrow, 'what's wrong?'

'I, uh, there's no way to, um, guarantee that you'll be found. In the alternative timeline.'

'I know Rodney, but we don't have a choice. I didn't save everyone on Atlantis last time only to have them perish now. And if you lose me, you might gain Zelenka or any one of the others.'

Rodney nodded absently, not really thinking about what he was doing. The Russian, crazy-haired scientist had been lost during an off-world mission some years before, but Rodney still missed him, like he missed Carson, Heightmeyer, like he'd missed Elizabeth.

'I'll, uh, go get started...' he trailed off, catching the look on Sheppard's face and turned, disappearing back into the control room.

Outside the sun rose higher, touching Elizabeth's hair with fire as she turned to back to him. 'I don't see a problem with resolving the timeline in our favour, Lis'beth,' he said adamantly, as soon as he had her attention.

' _In our favour?_ We've lost a lot of people over the years, John. I have no more right to a timeline where _I'm_ rescued than _they_ do. They deserve a roll of the dice too.'

'And if no one rolls double sixes?' he asked.

' _Someone_ will.'

'How do you know that?'

'I don't. But I have to _believe_ it, and so do you.'

He shook his head, 'I don't. I don't have to believe a damned thing except that _this_ timeline, the one we're standing in, _is the right one._ If we _do_ resolve it in our favour, or as close as we can get, you'll never even know. _I'll_ be the only one with the memory, from _him_.'

'And you can keep that from me? Forever?'

'If it means your peace of mind. I can.'

'And I'll know you're keeping secrets, John, what will that do for my peace of mind?' she cajoled softly.

'Fine! Then I won't tell him about _this conversation_ and he won't know. Nor will you!'

Then she said it, the words he'd hoped to skip right past. 'I know _now_.'

His shoulder sank in defeat. He took her hands in his. 'Yeah. I figured that one wouldn't get past you. Even if this timeline doesn't exist anymore... Sometimes, I wish you had less of a conscience.'

'No, you don't,' she corrected him, her tone certain.

The cocky fly-boy grin pulled at one side of his mouth. 'You gonna stop being right anytime soon?'

'I can't help it,' she smiled, 'I was born that way.'

The grin widened and he leaned in, kissed her once and stepped back, letting her go. 'I'll go check-in with Archer. Not a word. I swear.' And then he was gone, following Rodney into the quiet shadows of Atlantis.

Elizabeth looked out across the ocean, liquid gold shimmering, mixing with the blue, and drank in the sight. For all she knew, it would be the last one she would ever look upon. They were about to erase eight years of history and, potentially, herself along with it.

 _They'll have Zelenka back. Maybe. Or Allison, Joel... she thought, 'it's enough. It has to be.'_


	8. Chapter 8

__**_He watched her, the knowledge that he could lose her all over again burned into his mind. Together, they waited for their reality to shift, and wondered what would be left when it was over..._**

* * *

'I've managed to reverse-engineer the accident that sent you here. But you'll be going back to a reality bubble, and when the 'Gate system resolves the problem, you might experience some disorientation. It's not important, but it could fracture your memories so from the moment you land you have to start steering events in the direction of _this_ timeline,' McKay told him. He knew what Elizabeth's orders had been but he wasn't going to give up without a fight. He was a civilian, much as he cared about her, she was his boss, not his commander. And he didn't have Sheppard's sensibilities about the whole thing. 'There will be some variation when you return from what you knew...'

McKay was in full flow, John noted absently as he glanced around the 'Gateroom, leaning heavily on the crutches that Archer had insisted he use, in lieu of a wheelchair which had been met with adamant refusal. Elizabeth stood across the other side of the room, dark circles under her eyes.

'...however, the variations should be so slight as to be virtually unnoticeable, and nothing that should be realised at the macro level, you'd have to run a-'

'Yeah, I get it. Same universe. What about Elaras? If you've reverse engineered the accident, won't you have to send me back to the planet?'

'Uh, yeah,' Rodney looked more put out with the idea of sending John back into a hostile environment than the unexpected interruption. The Colonel could only assume that another six or so years in the Pegasus Galaxy had altered him even more than in the time he had known the physicist. 'There's nothing we can do about that; we might be able to alter your destination, but we have no idea how the 'Gate system would react. We'd have to change the 'Gate's own systems. Not even Elizabeth could make the alterations in the allotted time. If we don't get you back soon-'

'The timeline resolves with or without us, or the universe overloads with timelines.' The other Sheppard took over, the slightly older, slightly more scarred version of himself had a hard look in his eyes. John recognised it, like looking in a metaphorical mirror, he could see the turmoil and pain that hid behind the cold aloofness that the other man wore like a shroud. He was waiting for reality to collapse around him, either literally or figuratively, and it would be five years before Sheppard found out the truth of what happened to his future self the moment he stepped back through the 'Gate.

If he even made it back. Now that was a paradox that was guaranteed to put paid to _any_ future Sheppards. With Elizabeth in the room and what he suspected about their relationship in the future, that thought brought another on it's heels that he was quick to silence.

'Exactly,' Rodney finished. 'We should, uh-' he indicated the control room with a nod of his head and Elizabeth gave him one last look before she followed the scientist and Archer up the steps. They left the two Colonels alone.

'So, five years and I didn't make General yet?' Sheppard joked but, although his duplicate raised a slight smile, the humour never touched his eyes. Nearby, the 'Gate began to dial Elaras' past.

'Don't forget a word of what I told you. And... she never blamed you, you know. And you have to get over it, because if you don't the closest you and Elizabeth will be is neighbouring galaxies.'

'She's a good friend, a team mate-'

'Family, even? Yeah, I know, been there, said that. Then you're an idiot, Sheppard,' he replied bluntly. 'I'd rather take on a dozen Wraith ships than be Elizabeth's _friend_ for the rest of my life. Get over the guilt, and don't forget, wait to find her. If you go too soon-'

'She might not even be there. I know. Good luck.' He held out his hand, and the Colonel took it.

'Likewise.'

Gritting his teeth, Sheppard let go of the crutches, his double taking them, and lifted his weapon. With a watery rush, the wormhole established and, with a nod to the faces watching from the control room, he turned, heading for the 'Gate. He glanced back once, to see her, standing on the balcony, watching him depart. It was an image he would have to keep fixed in his mind, it was the only one he would likely have for some time.

He turned back, stalking determinedly through the event horizon, listing badly to the left, weapon raised. He wouldn't have much time on the other side to dial Atlantis. He disappeared and the Gate fell silent, the whine of the generators fading as the extra power was withdrawn from the system.

The future John Sheppard looked up, his gaze locking with hers as she stared down from her balcony. This could leave her in Asuran hands _forever_. He read the fear in her eyes, but could do nothing to assuage it. he could only hope Sheppard was smarter than him and carried on searching until he found her.

The lag time the Ancients built in was ending and as he watched, his brain spun. He saw Elizabeth fall and ran for the stairs, but he didn't make it. Instead of the steps, he was in the control room and Atlantis was under attack. The disorientation and his old memories faded fast. Elizabeth came running up the steps. 'The ZPM is in place! Rodney! Do you have those shield modifications ready?'

'Almost!' he shouted above the din of darts and the shuddering, tearing groans of Atlantis as they attacked her.

'John!' Elizabeth caught his arm, looked up into his face. 'Are you alright?'

He hesitated for a moment then pulled her into his arms, holding her tight for one brief moment. He pulled away, holding her by the shoulders.

'John?' she queried, confused. 'What's going on?'

'You're alright,' he said, then shook his head, 'I don't know why I said that.'

'It doesn't matter. But none of us are going to be okay much longer if Rodney doesn't have time to finish those modifications!'

'I know. Jumpers, go shoot down Darts. Got it,' he turned, paused and glanced back. She caught his gaze.

'Luck, John,' she mouthed, almost silently.

'Stay safe,' he whispered and then he was gone.

It wasn't until much later, when the attack was over, the Apollo and the Thor hanging in orbit and the strengthened shield in place around the city, that he found out the cause for his disorientation. Elizabeth caught up with him after the debrief, she was on her way to call the Apollo and speak with Carter.

'She'll be better at analysing the information, but John, I think you should hear this first.'

'Hear what?' he asked as she led him into her office and closed the door. To put space between them and everyone else she waved him onto the balcony and slid the door shut there too, cutting them off. He frowned, waiting for her to turn round. 'Okay, Lis'beth, what's this all about?'

She paused for a moment, biting her lip and then drew a breath. 'I think I've told you before that my nanites load-share, that is, information is passed between them in single bytes every millisecond. It means that each nanites has part of the information and if any are damaged, it can be reconstructed; its even more accurate with the use of human mind because we weight probabilities differently, the nanites weigh them all the same. What I mean is-.'

'They're just as likely to pick a wrong choice as a right one, yeah, I understand. So?'

'So, earlier today, in the middle of the attack, you... experienced some disorientation. With the fractured information from my nanites, plus my own experience and yours, I've extrapolated the most likely cause for your confusion.'

'I'd almost forgotten,' he admitted, running one hand through his hair. 'What's the cause?'

'We're in an alternate timeline. This afternoon, during the attack, the timeline shifted around us. For some reason you were rendered, shall we say, _temporarily_ immune, I don't know why, there's more information that needs analysing. That's why I need Carter's help, she understand the nanites better than anyone, even Rodney,' she added, with a wry smile.

John loked confused, 'that doesn't make any sense. We've been in the middle of this mess for over a year now, why would I remember this war if it only started today?'

'It didn't, the timeline changed today, but once it changed, it changed our past as well as our present,' she said. 'As the timelines shifted, my nanites were passing information back and forth, the conflicting information was logged and archived and flagged for my attention. It was only after the attack was over I had time to process what I had learned. The conflicting information came from another timeline, another _me_. One who wasn't at war.'

'Wait,' Sheppard frowned, squeezing his eyes shut for a second and rubbing his brow.

'Headache?' Elizabeth enquried softly.

'Yeah,' he muttered.

'I think we're central to the change, John, I think some part of you is clinging to that alternative timeline. It doesn't make sense, you shouldn't be able to, but I have no other explanation.'

'Do you remember? I-I found you on that planet? Pulled out your pod and... no, I mean, we called _Keller_ and- The point is,' he said, shoving aside the conflicting memories, 'is that I got the information where to find you, _when_ to find you, from a future version of myself. I met you, but...'

'But Atlantis wasn't at war? The Wraith weren't overrunning the galaxy? We weren't on the verge of annihalation?'

'Yeah,' he murmured, his face grave as he began to realise the magnitude of waht had gone wrong, 'something like that.'

Elizabeth shook her head slowly, 'this is wrong, John, it's all wrong. We have to fix this. We have to talk to Carter and the SGC, we have to do it now.'

'But what does it matter? My past self already returned to his time, I remember it, what can we do with the information now?'

'I have an idea about that,' she replied, 'and you're not going to like it.'

Elizabeth's nanites continually passed information back and forth between them, that included alternate timeline nanites as they faded from existence.

Their timeline _had_ been changed, Elizabeth _was_ rescued, but their world had gone to hell with Atlantis in the Milky Way, the Wraith running rampant in the Pegasus galaxy and even the Alliance fought _with_ Earth now, not against it. The question was, when they all finally realised the truth, was what they hell had gone wrong?


	9. Chapter 9

_**He has two years to wait, two years to let the guilt go. He knows he should talk to someone, but the risk of contamination to the timeline is too great. This is a journey he must make alone...**_

* * *

Sheppard made it to Atlantis, almost falling through the Gate, thankful to be back and blissfully unaware of the chaos he had left behind in the future. Someone called for a medic as he staggered and ended slid to the floor. When a hand touched his shoulder, he opened his eyes and saw a blonde head and blue eyes staring down at him. 'Colonel Carter?' he queried. Not the woman he wanted to see, but a surprising reassurance all the same.

'Looks like you've gotten yourself in trouble again, Colonel,' she smiled. When he tried to move, she firmly pushed him back down. 'Medical team's on it's way.'

'I've already been treated,' he told her. Carter raised an eyebrow and he sighed, relaxing against the cold metal floor. 'The wormhole drew so much power it flung me into the future. About five or six years, I couldn't really say. As soon as they realised who I was, they kept me isolated.' He had already decided on his lies before he even left the other Atlantis. His story needed to make sense, he couldn't let anyone stop him from keeping the timelines on track.

'Smart move,' Carter noted, but her gaze didn't leave his and he wondered if his head had suddenly become transparent, exposing all his thoughts. 'I'll expect a full report when you're cleared by Dr Keller.'

'Where's Woolsey?'

'Shore leave. Family emergency, and with you gone, the SGC gave the Apollo clearance to stay here for a few weeks. I've been given temporary charge of Atlantis.'

He could hear the wheels of the gurney, Keller's quick steps and her light voice, calling out. He nodded, smiled. 'Good to have you back, Colonel.'

'Likewise, Colonel,' she grinned.

* * *

Lying in the infirmary, five years seemed a long time to wait to find out his fate, or rather, the fate of his future counterpart. He could only hope that, wherever he had landed in this timeline, it was somewhere near Elizabeth.

 _Elizabeth._

She was out there, somewhere. Not safe, far from it in fact. but she was alive, and would remain so, he could only hope, through the long months that followed. Two years, when compared against those five, seemed longer, more arduous, and he wondered how he would survive when each hour crawled past as he lay there, staring at a familiar ceiling.

'John.' It was Teyla. A constant visitor, both with and without her son, who was growing quickly into a sturdy little lad with his father's dark hair and his mother's golden eyes. He turned towards her voice, grateful for the distraction. 'How are you feeling today?'

'I'm alright. I just wish Keller would let me out of here. There's nothing really wrong with me anymore.'

The Athosian smiled, inclining her head slightly and he recognised the look. She used it when she thought her team mates were being foolish. It wasn't the first time she had directed it at him, and it wouldn't be the last. 'You will be allowed out of the infirmary when you are well. Dr Keller is wise in the ways of such things. However, when she does allow you to leave your bed, will you join us for dinner?'

'Love to.' Another distraction and John seized it eagerly. Not that dinner with Teyla and the family was without its charms. The boy, Torren, was a humorous kid who seemed to find his uncle John an amusing fellow. 'Did you ask Rodney?'

'Yes. Dr McKay is also convalescing and I thought it would take his mind off his, shall we say, his current _disadvantage_. It was his right arm that was broken, and he is currently whining, at length, over the speed with which his assistants are following his instructions.'

'Poor kids,' John remarked with a crooked smile. McKay had a habit of being surprisingly brave when it was needed, of putting aside his woes to deal with the situation in hand. but when the crisis had passed and he was free to lament at will, he very often did.

Although- he frequently moderated his rants whenever Dr Keller was around. John, like everyone else on Atlantis, would have to have been made out of stone not to notice the way Rodney felt about Jennifer. It was another distraction and he added them up in his head; they could fill up the time, save him from going crazy.

Silence had fallen, not uncomfortable, for it never was with those closest to him on Atlantis. But the quiet allowed his thoughts to intrude to again, and the image of Elizabeth, at the mercy of Oberon, flashed across his mind. Leaving almost anyone to Oberon's tender mercies was unthinkable, the idea that Elizabeth would have to endure it for many months yet to come, was intolerable.

'There is something you are not telling us, isn't there?' Teyla's voice was filled with compassion. Whatever it was Sheppard was choosing to keep to himself was just as obviously causing him grief. She wished she could alleviate some of his concerns, but without the Colonel being more forthcoming, she was at a loss to know how to help him.

'Yes.' He admitted without preamble. He couldn't tell her, he never would, but the sheer relief he felt at letting someone know he had a secret to keep, was incredible. He sank back against the pillows with a sigh, allowing his eyes to drift shut.

Teyla waited for a moment, wondering if he would say more, but the conversation was over. She stood for some minutes more and then spoke again. 'I am sure you are very tired, I will leave you. Shall I come again in the morning?'

He opened his eyes, the ghost of a smile touching his mouth. 'You betcha.'

'I will bring Torren. He has missed you.'

'Well, I'm a missable kinda guy,' the smile was broader now, and there was a comfort in that, to see his old self shining through. Whatever secrets John harboured, she was sure that they were not too heavy for the good of his soul. And if they were, perhaps he would relieve himself of his burdens then.

* * *

When he was finally allowed out, John found himself on the balcony outside her office first. It was a place he'd often found solace, and a kind of peace, inbetween the chaos of one crisis and the next. Breathing in the cool salt air, he listened to the waves crashing distantly against the city below. It's natural to come here, like going out to the pier when he thinks of Carson. Places he associates in Atlantis with the people they've lost. It didn't take long for him to end up on the balcony again, and again.

Behind him the door slid open and he heard her step out onto the balcony. It wasn't fair to Carter, he realised. She was a good person, a great leader and yet, every time he saw her in that office, he hated it. She deserved his loyalty, not his contempt. 'I didn't realise anyone was out here,' she said quietly, joining him at the rail.

Carter wasn't often out here. A while after Elizabeth first went missing, if things went badly, or were quiet, John would find his way out here and she never wanted to intrude on that. Back at the SGC, when Jack had gone missing, no one else came in to lounge or fiddle. Not even her team mates. It Jack's habit, Jack's seat. She felt like this about the balcony, and it was only after Elizabeth's Replicated self had turned up with copies of Sheppard, McKay, Teyla and Ronan along, informing him Weir was dead, that her quarters had been freed up.

Oddly, they were still empty. It would take time, Carter realised. Taking over Weir's office had been bad enough, she was content to leave her quarters empty. Oddly she was sure John never went there, it was always here, on the balcony, looking over the waves. She looked out over the ocean, taking in a deep breath. 'Everytime I come out here, not often I'll admit, I can see why Dr Weir liked it here.'

He nodded, his fingers unconsciously tightening on the rail. 'She was almost a part of the city itself. An alternate timeline Elizabeth waited in this city for ten thousand years just so we could land here safely. She gave her life for the Expedition. I don't think there's a version of her that would do less.'

Carter nodded, hesitating, as if she wasn't sure whether to speak. 'Off the record, John?'

He paused but nodded slowly, turning to look at her. 'Go on.'

'Since you've come back, you've been spending more time out here. Did you learn something out there? If you've got a lead, a plan, anything, I'm wiling to listen. Dr Weir and I didn't always see eye to eye but we believed in the same things. If I could bring her back, I would throw the resources of Atlantis and the Apollo into that mission. I know you don't believe she's dead, not really.'

'My report says I was isolated. So I wouldn't affect future timelines.'

'I know,' she said, 'I _also_ know that sometimes what happens out there, offworld, stays out there. You don't have to feel guilty, John, I read the reports, you did everything you could and Dr Weir made her own choices,' she half smiled, 'she always did.'

He nodded, wondering if he should say something but Sheppard had been adamant. Involving just one more person could send the future in a completely different direction. As much as he wanted the help, especially from someone as smart and resourceful as Carter who had already experienced changing timelines, he wouldn't play roulette with Elizabeth's life. He _couldn't._ He had already done that once too often, and he had lost.

So he let Carter go without a word.

 _Lose the guilt_ , his counterpart told him, and Carter now too, although he refused to speculate _why_ that should be so important. He was never one for introspection but he's thinking of guilt now, and his in particular. All the people who've died, all those he felt guilty over, and all those he caused.

The numbers don't necessarily tally.

He fixes the names in his head, ending with Elizabeth's. He's got nothing else to do whilst he's marking time to the first fork in the road, this is the only problem he can tackle, so he does. For a little while. By the time John left the balcony, he felt calmer, two years feeling more manageable than they did back in the infirmary.


	10. Chapter 10

**_Like a prisoner yearning for freedom, he'd done his time and now the day was here, and so was she, waiting on the other side of the door..._**

* * *

The final days crawled by as John Sheppard waited, watching for the moment he could allow time to flow on its destined course, or divert the river in the direction he needed it to go. Elizabeth had lain in Oberon's hands long enough. John stood outside on the balcony, looking out over the night-dark ocean, his fingers curling around the icy rail. The next time he watched twilight fall over the city, she would be back within its well-loved walls. One way or another, he was bringing her home today.

By the time dawn crept over the horizon, he was standing in the control room, his eyes on the 'Gate, gleaming below in the warm light. They were due to leave in an hour for H2-714, a small, unimportant planet to most, it's only grace being it's location, perfect for a second base, if it were uninhabited. He already knew it was.

For the last time, Sheppard waited, counting down the minutes.

'What's he doing?'

Pierson looked over at McKay, breaking his gaze from the Colonel's back. 'I'm not sure sir, he was here when I came on shift, and he's stood there ever since, just watching the 'Gate. Waiting.'

'John?' It was Teyla, stepping carefully around his mute form to look up into his face. He looked at peace, centred in a way she had never seen him before. He looked away from the 'Gate and smiled at her as Woolsey appeared in the Gateroom below, heading for the stairs.

'Ready?' he asked.

'I am,' but still the puzzlement remained although he didn't seem to notice.

'Good,' he twisted round with a grin, scanning the room for his team-mates. 'Okay guys, let's move out.'

Ronan eyed him but grunted an affirmative and McKay came jogging down the stairs, trailing questions. Sheppard ignored all requests for more information, bypassing direct enquiries with a simple, _I woke up early, that's all._

The 'Gate dialled, engaged and with a whoosh the wormhole established itself. The team unconsciously arranged themselves in formation, moving forward onto an unknown world. They stepped into a lush forest, verdant and green with life. It felt like the temperate woodlands of Earth, and Rodney managed to raise a smile as they moved deeper into the shade under the trees. 'Hey, feels just like home.'

'Yeah,' but Sheppard seemed distracted, scanning the forest around them.

'What's the matter? Did you hear something? I'm not detecting any signs of movement,' McKay lifted the tablet on his arm, but there were no signs of life. He looked up, around. Not a single creature disturbed the leaves.

'Nope. Just being cautious, that's all.'

'You sure? Cos you've been acting... odd the past few days.'

'What are you talking about, Rodney?' It was quick to start, but Sheppard sounded expasperated already.

'Dr McKay is right, J-' Teyla began.

'There!' Sheppard barked, cutting her off. Ahead, through the trees, something glinted in the sunlight.

'I see it, too.' Teyla rose on tiptoe, looking in the same direction. She glanced at John, the exultation in his face as well as his voice, as if he'd known this would be here all along. 'John...?' she questioned in a warning tone.

But he ignored her, gesturing ahead. 'C'mon, let's check it out,' he called to the others, waving them in the right direction. Rodney and Ronan turned, heading towards them, whilst Sheppard forged ahead, Teyla close behind.

It stood in a clearing, a dome-shaped building made of glass and metal. It stood silent, as if abandoned and there was evidence of some kind of battle. Scorched earth and broken windows. But Sheppard wasted little time with the view, lifting his weapon to scan the surrounding trees, but not a soul moved, not a leaf stirred and he walked on, across open ground to the sealed metal door.

'McKay! Think you can open this?'

'Gee, I don't know, let me see... nope, sorry, it's too far away,' Rodney puffed his way over to where Sheppard and Teyla were standing. 'What on earth possessed you to-?'

'Just open it, McKay!' came the reply through gritted teeth.

'No!' It was Teyla. 'John, what is going on? You have been acting strangely these past few days, and now you run into a potentially dangerous situation without stopping to think. What is going on?'

John looked at her, before regarding Ronan and Rodney each in turn. The resolve in their faces wasn't new, his team was stubborn, they had their principles and they had to know why they there were heading somewhere before abandoning themselves to it whole-heartedly. He knew they weren't going to help him without some kind of explanation. He sighed, turning his back on the door and leaning against it.

'I didn't tell you everything about the time I was lost on Elaras. What I learned- Well, I could barely live with myself, I couldn't ask any of you to- And I couldn't risk the timeline, the less people who knew, the better. Events needed to play out the way they were supposed to, I couldn't risk someone else contaminating this reality.'

'What? What are you talking about?' It was Rodney.

'When I went forward in time. I wasn't kept isolated from the rest of Atlantis. I met myself, you Rodney, a few new faces and... Elizabeth.'

They stared at him, Rodney taking an automatic step forward. 'Elizabeth?' he queried, repeating her name slowly. 'As in, _our_ Elizabeth? Elizabeth Weir?'

'Yes. Oberon lied to his people, he kept Elizabeth alive,' he turned to look at the smooth metal door, laying a hand flat against the sun-warmed surface. 'If events have played out the way they should have, she's in here. Somewhere... What are you doing?'

The question was directed at McKay, who had brushed him aside, dumping his gear on the ground and was pulling out a bundle of wires and the computer from his pack. 'Getting her out, what does it look like? I think we've left her here long enough, don't you?' Anger laced his voice, and it latched on to Sheppard's residual guilt, biting deep. What he had done had been necessary, but that didn't negate the past two years and what she must have endured.

He pushed the thought aside as the door slid open. Inside, light poured through the glass walls and floor above. The room was extensive, disappearing towards the other end of the building, open spaces were interspersed with workstations and equipment was scattered everywhere as if the laboratory had been abandoned in a hurry.

Sheppard raised his weapon, stepping inside the silent building, the others falling into line behind him. They spread out, scanning the room for any sign of a familiar face they thought long since lost.


	11. Chapter 11

_**Suspended in nothingness, she travelled within her own mind until something alerted her to their presence. At first, she wondered if they were merely memories, until one of them turned and a familiar face looked her way. A sob of relief echoed in her mind. But was it only a dream?**_

* * *

The world was white, with the barest hint of blue. She hung, suspended at its centre, like an object in space. Oberon and his cronies were long gone, leaving her here. Or maybe they were still around, creating this place like a virtual world inside her head, making her believe she was really there. It _felt_ real, but then Oberon had a habit of making real those things that weren't.

Terrible things- things that once lived only in her nightmares.

So she played games, building her own world inside her head, a place she could retreat to whenever the nightmares came. Her world was an ocean and on it lay a gleaming city, like a gem, with spires that touched the heart of the sky. People lived there, names and faces she'd known so long now, that her heart ached whenever she had to leave them, leave the city and go back to the Asuran world.

Sometimes she wondered if Atlantis was real, or just another dream. She usually followed up that piece of folly with a mental slap, reminding herself of the time when Atlantis she thought Atlantis imaginary, a time when someone had called her back to it, his shadow falling into every corner of the imaginary world the nanites had placed her in.

He had never given up on her back then, so she hung inside the white bubble, listening for his voice again, watching for his shadow.

Waiting.

And then something happened. She didn't hear, or see, or feel anything, but somehow she knew. _He was here._

The voices came later, following the footsteps, hushed and low. She listened, straining with ears not her own to pick out the slightest sound. For the first time since she had awoken inside the white-blue light, she reached out, tapping into other eyes, turning them to find the source of the sounds intruding on her world.

That was where his shadow fell, cast by sunlight pouring in through windows so tall and wide they replaced the wall. It reminded her of Atlantis, the world within reflecting the one without. She followed the shadow to find him. He was older than she remembered, his eyes darker. She remembered his companions too. His team. His family.

He was their leader, their direction, their will. The woman, filled with a quiet peace, their conscience given form. And the scientist, the mind, walking with the warrior, their strength. She watched them move as one, and longed to leave the place where she hung, to join them. She wanted, so badly, for her place to be there.

But she had no idea if it was. She didn't know _where_ she belonged anymore.

 _John_.

His name was John.

The memories came thick and fast, bubbling to the surface of her mind. The Atlantis within became more solid, more real, as her memories poured into it.

The city.

It was almost sobbed aloud with relief. Her waiting had not been in vain. They had come. She drew in a mental breath, before sending a wave of communication along every network she could reach within the laboratory, hoping something, anything, would spark a signal.

 _I'm here, John, I'm here!_


End file.
